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Package 281/294HostnameOS / ArchBUILDCHECKBUILD BIN
topGO 1.10.1
Adrian Alexa
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/topGO
Last Changed Rev: 35382 / Revision: 38965
Last Changed Date: 2008-11-17 14:19:26 -0800 (Mon, 17 Nov 2008)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK [ WARNINGS ] OK 
Package: topGO
Version: 1.10.1
Command: /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R CMD check --no-vignettes topGO_1.10.1.tar.gz
StartedAt: 2009-04-18 18:31:47 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 18:34:22 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 155.3 seconds
RetCode: 0
Status: WARNINGS
CheckDir: topGO.Rcheck
Warnings: 1

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/topGO.Rcheck'
* using R version 2.8.1 Patched (2009-03-18 r48200)
* using session charset: ASCII
* checking for file 'topGO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'topGO' version '1.10.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'topGO' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.sigGroups.weight2: no visible binding for global variable
  'nodesUpSubgraph'
GOglobalTest,classicExpr: no visible global function definition for
  'p.value'
GOglobalTest,classicExpr: no visible global function definition for
  'globaltest'
GOtTest,classicScore: no visible global function definition for
  'alternative'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  nodesInInducedGraph
Undocumented data sets:
  geneList topDiffGenes
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* creating topGO-Ex.R ... OK
* checking examples ... OK
* creating topGO-manual.tex ... OK
* checking topGO-manual.tex using pdflatex ... OK

WARNING: There was 1 warning, see
  /Users/biocbuild/bbs-2.3-bioc/meat/topGO.Rcheck/00check.log
for details

topGO.Rcheck/00install.out:

* Installing *source* package 'topGO' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: graph
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: SparseM
Package SparseM (0.79) loaded.  To cite, see citation("SparseM")

Attaching package: 'SparseM'


	The following object(s) are masked from package:stats :

	 model.response 


	The following object(s) are masked from package:base :

	 backsolve,
	 chol 

Creating a new generic function for "print" in "topGO"
** help
 >>> Building/Updating help pages for package 'topGO'
     Formats: text html latex example 
  GOFisherTest                      text    html    latex
  GOKSTest                          text    html    latex
  GOdata                            text    html    latex   example
  GOglobalTest                      text    html    latex
  annFUN                            text    html    latex   example
  buildGOgraph.topology             text    html    latex
  buildLevels                       text    html    latex   example
  classicCount-class                text    html    latex   example
  classicExpr-class                 text    html    latex   example
  classicScore-class                text    html    latex   example
  elimCount-class                   text    html    latex   example
  elimExpr-class                    text    html    latex   example
  elimScore-class                   text    html    latex   example
  getPvalues                        text    html    latex   example
  getSigGroups                      text    html    latex   example
  groupGOTerms                      text    html    latex   example
  groupStats-class                  text    html    latex   example
  inducedGraph                      text    html    latex   example
  mapGenes2GOgraph                  text    html    latex   example
  parentChild-class                 text    html    latex   example
  printGenes-methods                text    html    latex
  printGraph-methods                text    html    latex   example
  reverseArch                       text    html    latex   example
  topGO-package                     text    html    latex
  topGOdata-class                   text    html    latex   example
  topGOresult-class                 text    html    latex
  weightCount-class                 text    html    latex   example
  weightScore-class                 text    html    latex
** building package indices ...
* DONE (topGO)